Coral reefs are threatened worldwide by a variety of natural and human-induced stressors; anomalous temperatures are presently among the most serious threats by causing extensive coral bleaching. Amphistegina spp. exhibit similar bleaching as corals in the presence of photo-oxidative stress induced by either light or temperature, especially during times of maximum solar irradiance. At 11 islands (34 sampling sites) in the North Ari Atoll in the Maldives, bleaching in Amphistegina was observed a few weeks before the onset of an extensive El Niño-related coral bleaching that was more severe than expected for this region. Assessment using the Amphistegina Bleaching Index (ABI) showed that the proportions of bleached specimens of Amphistegina in April–May 2015 can be explained by photo-inhibitory stress associated with temperatures exceeding 30°C during peak seasonal solar irradiance and water transparency. Importantly, the ABI indicates that environmental conditions are suitable for Amphistegina and other calcifying symbioses at most of the investigated sites, and that either chronic or relatively recent onset of photo-oxidative stress was present at the time of sampling. The observed bleaching in Amphistegina further demonstrates the potential of these unicellular protists to identify stressors in coral reefs; such applications should be considered in future reef-management plans.